Class: BiologicalProcess

URI: bp:BiologicalProcess

erDiagram BiologicalProcess { string label string description stringList synonyms string id } GeneMolecularActivityRelationship { } MolecularActivity { string id string label } Gene { string id string label } ChemicalEntity { string id string label } BiologicalProcess ||--|o BiologicalProcess : "subclass_of" BiologicalProcess ||--}o ChemicalEntity : "inputs" BiologicalProcess ||--}o ChemicalEntity : "outputs" BiologicalProcess ||--}o MolecularActivity : "steps" BiologicalProcess ||--}o Gene : "genes" BiologicalProcess ||--}o GeneMolecularActivityRelationship : "gene_activities" GeneMolecularActivityRelationship ||--|o Gene : "gene" GeneMolecularActivityRelationship ||--|o MolecularActivity : "molecular_activity"

Inheritance

NamedEntity
- BiologicalProcess

Slots

Name	Cardinality and Range	Description	Inheritance
label	0..1 String	the name of the biological process	direct
description	0..1 String	a textual description of the biological process	direct
synonyms	* String	alternative names of the biological process	direct
subclass_of	0..1 BiologicalProcess	the category to which this biological process belongs	direct
inputs	* ChemicalEntity	the inputs of the biological process	direct
outputs	* ChemicalEntity	the outputs of the biological process	direct
steps	* MolecularActivity	the steps involved in this biological process	direct
genes	* Gene		direct
gene_activities	* GeneMolecularActivityRelationship	semicolon-separated list of gene to molecular activity relationships	direct
id	1 String	A unique identifier for the named entity	NamedEntity

Usages

used by	used in	type	used
BiologicalProcess	subclass_of	range	BiologicalProcess

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/ontogpt/biological_process

Mappings

Mapping Type	Mapped Value
self	bp:BiologicalProcess
native	bp:BiologicalProcess

LinkML Source

Direct

name: BiologicalProcess
from_schema: https://w3id.org/ontogpt/biological_process
is_a: NamedEntity
attributes:
  label:
    name: label
    description: the name of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    domain_of:
    - BiologicalProcess
    - NamedEntity
  description:
    name: description
    description: a textual description of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    domain_of:
    - BiologicalProcess
  synonyms:
    name: synonyms
    description: alternative names of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
  subclass_of:
    name: subclass_of
    description: the category to which this biological process belongs
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    domain_of:
    - BiologicalProcess
    range: BiologicalProcess
  inputs:
    name: inputs
    description: the inputs of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
    range: ChemicalEntity
  outputs:
    name: outputs
    description: the outputs of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
    range: ChemicalEntity
  steps:
    name: steps
    description: the steps involved in this biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
    range: MolecularActivity
  genes:
    name: genes
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
    range: Gene
  gene_activities:
    name: gene_activities
    description: semicolon-separated list of gene to molecular activity relationships
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    domain_of:
    - BiologicalProcess
    range: GeneMolecularActivityRelationship
tree_root: true

Induced

name: BiologicalProcess
from_schema: https://w3id.org/ontogpt/biological_process
is_a: NamedEntity
attributes:
  label:
    name: label
    description: the name of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    alias: label
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    - NamedEntity
    range: string
  description:
    name: description
    description: a textual description of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    alias: description
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: string
  synonyms:
    name: synonyms
    description: alternative names of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: synonyms
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: string
  subclass_of:
    name: subclass_of
    description: the category to which this biological process belongs
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    alias: subclass_of
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: BiologicalProcess
  inputs:
    name: inputs
    description: the inputs of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: inputs
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: ChemicalEntity
  outputs:
    name: outputs
    description: the outputs of the biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: outputs
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: ChemicalEntity
  steps:
    name: steps
    description: the steps involved in this biological process
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: steps
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: MolecularActivity
  genes:
    name: genes
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: genes
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: Gene
  gene_activities:
    name: gene_activities
    description: semicolon-separated list of gene to molecular activity relationships
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    multivalued: true
    alias: gene_activities
    owner: BiologicalProcess
    domain_of:
    - BiologicalProcess
    range: GeneMolecularActivityRelationship
  id:
    name: id
    annotations:
      prompt.skip:
        tag: prompt.skip
        value: 'true'
    description: A unique identifier for the named entity
    comments:
    - this is populated during the grounding and normalization step
    from_schema: https://w3id.org/ontogpt/biological_process
    rank: 1000
    identifier: true
    alias: id
    owner: BiologicalProcess
    domain_of:
    - NamedEntity
    - Publication
    range: string
    required: true
tree_root: true